A High Time-Efficient Missing Tag Detection Scheme for Integrated RFID Systems.

Missing tag incidents are common in RFID-enabled supply-chain and warehousing scenarios due to cargo theft and employee error operations, which may lead to serious economic losses or potential safety hazards. On the premise of ensuring the accuracy of missing tag detection, this paper aims to improve the time efficiency in an integrated RFID system. Unlike prior work focusing on detecting missing items from a large number of homogeneous tags that are monitored by a single reader, one integrated RFID system possesses multiple readers to communicate with the heterogeneous tags, which have different categorical attributes. In addition, the prior work required repeating the execution several times to capture the missing tags in assorted categories, which is of low time efficiency. Thus, a protocol called Multi-reader Missing Tag Detection (MMTD) is proposed to capture the missing tag quickly and reliably, which can detect missing tags from different categories in a parallel manner and is much more time-efficient than previous work. MMTD has two major advantages compared to prior work: (i) It leverages the knowledge of the spatial distribution of tags to divide up a difficult detection task into several lightweight tasks, which are shared by multiple readers. (ii) It personalizes the time frame of the reader based on the tag population to optimize the utilization of the communication channel. The final simulation results reveal that MMTD is the best in time-efficiency among the comparison protocols, and MMTD outperforms the other missing tag detection protocols by at least 1.5× in the Integrated RFID scenarios.

Scalable Distributed Hashing for Approximate Nearest Neighbor Search.

Hashing has been widely applied to the large-scale approximate nearest neighbor search problem owing to its high efficiency and low storage requirement. Most investigations concentrate on learning hashing methods in a centralized setting. However, in existing big data systems, data is often stored across different nodes. In some situations, data is even collected in a distributed manner. A straightforward way to solve this problem is to aggregate all the data into the fusion center to obtain the search result (aggregating method). However, this strategy is not feasible because of the prohibitive communication cost. Although a few distributed hashing methods have been proposed to reduce this cost, they only focus on designing a distributed algorithm for a specific global optimization objective without considering scalability. Moreover, existing distributed hashing methods aim at finding a distributed solution to hashing, meanwhile avoiding accuracy loss, rather than improving accuracy. To address these challenges, we propose a Scalable Distributed Hashing (SDisH) model in which most existing hashing methods can be extended to process distributed data with no changes. Furthermore, to improve accuracy, we utilize the search radius as a global variable across different nodes to achieve a global optimum search result for every iteration. In addition, a voting algorithm is presented based on the results produced by multiple iterations to further reduce search errors. Theoretical analyses of communication, computation, and accuracy demonstrate the superiority of the proposed model. Numerical simulations on three large-scale and two relatively small benchmark datasets also show that the SDisH model achieves up to 44.75% and 10.23% accuracy gains compared to the aggregating method and state-of-the-art distributed hashing methods, respectively.

Fast kNN Search in Weighted Hamming Space With Multiple Tables.

Hashing methods have been widely used in Approximate Nearest Neighbor (ANN) search for big data due to low storage requirements and high search efficiency. These methods usually map the ANN search for big data into the k -Nearest Neighbor ( k NN) search problem in Hamming space. However, Hamming distance calculation ignores the bit-level distinction, leading to confusing ranking. In order to further increase search accuracy, various bit-level weights have been proposed to rank hash codes in weighted Hamming space. Nevertheless, existing ranking methods in weighted Hamming space are almost based on exhaustive linear scan, which is time consuming and not suitable for large datasets. Although Multi-Index hashing that is a sub-linear search method has been proposed, it relies on Hamming distance rather than weighted Hamming distance. To address this issue, we propose an exact k NN search approach with Multiple Tables in Weighted Hamming space named WHMT, in which the distribution of bit-level weights is incorporated into the multi-index building. By WHMT, we can get the optimal candidate set for exact k NN search in weighted Hamming space without exhaustive linear scan. Experimental results show that WHMT can achieve dramatic speedup up to 69.8 times over linear scan baseline without losing accuracy in weighted Hamming space.

Mutation spectrum of COL1A1/COL1A2 screening by high-resolution melting analysis of Chinese patients with osteogenesis imperfecta.

High-resolution melting (HRM) analysis has been shown to be a time-saving method for the screening of genetic variants. To increase the precision of the diagnosis of osteogenesis imperfecta (OI), we used HRM to explore COL1A1/COL1A2 mutations in 87 Chinese OI patients and to perform population-based studies of the relationships between their genotypes and phenotypes. Peripheral blood samples were collected from the 87 non-consanguineous probands. The coding regions and exon boundaries of COL1A1/COL1A2 were detected by HRM and confirmed by Sanger sequencing. The functional effects of mutations were predicted through bioinformatic tools. Mutations were detected in 70.3% of familial cases and 40% of sporadic cases (p < 0.01). Compared with COL1A1 mutations, patients with COL1A2 mutations were more prone to severe phenotypes. Helical mutations (caused by substitution of the glycine within the Gly-X-Y triplet domain) were more likely to occur in patients with type III and IV (p < 0.05). Haploinsufficiency mutations (caused by frameshift, nonsense, and splice-site mutations) appeared more frequently in patients with type I (p < 0.05). Compared with the Sanger sequencing and whole exome sequencing (WES), HRM was found to reduce total costs by 78%- 80% in patients who had a positive HRM separate melting curve. Our findings suggest that HRM would greatly benefit small and understaffed hospitals and laboratories, and would facilitate the accurate diagnosis and early treatment of OI in remote and less developed regions.

iTRAQ-based quantitative proteomic analysis reveals potential early diagnostic markers in serum of acute cellular rejection after liver transplantation.

Liver transplantation (LT) is the most effective treatment method for advanced stage liver disease but acute cellular rejection (ACR) seriously affects the prognosis of LT. To discover novel diagnostic biomarkers of ACR after LT, Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-based mass spectrometry was performed to characterize alterations of serum proteins among patients validated to be pathologically ACR or pathologically no-ACR after LT and healthy controls. As a result, 10 differentially expressed proteins were found out between the ACR group and the No-ACR group; 88 differentially expressed proteins were found out between the ACR group and the Healthy Control group; 39 differentially expressed proteins were found out between No-ACR group and Healthy Control group. After analysis and ELISA validation, the results showed that CFHR1, CFHR5 and CFH could be candidate protein biomarkers for the early diagnosis of ACR after LT.

EasyLB: Adaptive Load Balancing Based on Flowlet Switching for Wireless Sensor Networks.

Load balancing is effective in reducing network congestion and improving network throughput in wireless sensor networks (WSNs). Due to the fluctuation of wireless channels, traditional schemes achieving load balancing in WSNs need to maintain global or local congestion information, which turn out to be complicated to implement. In this paper, we design a flowlet switching based load balancing scheme, called EasyLB, by extending OpenFlow protocol. Flowlet switching is efficient to achieve adaptive load balancing in WSNs. Nevertheless, one tricky problem lies in determining the flowlet timeout value, δ . Setting it too small would risk reordering issue, while setting it too large would reduce flowlet opportunities. By formulating the timeout setting problem with a stationary distribution of Markov chain, we give a theoretical reference for setting an appropriate timeout value in flowlet switching based load balancing scheme. Moreover, non-equal probability path selection and multiple parallel load balancing paths are considered in timeout setting problem. Experimental results show that, by setting timeout value following the preceding theoretical reference, EasyLB is adaptive to wireless channel condition change and achieves fast convergence of load balancing after link failures.

Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice.

OBJECTIVE: The benefits of IL-35 treatment have been verified in multiple animal models of diseases, while its influence on T cells immunity under normal condition still needs to be elucidated. The present study was designed to investigate the effects modulating IL-35 levels in vivo and in vitro on T cells, response and also the effects on T cells subsets in normal mice. METHODS: A plasmid pMSCV-IL-35-GFP carrying mouse linear IL-35 fragment with two subunits joint together was constructed and the heterodimer expression was confirmed. Normal mice were randomly divided into three groups and received an intravenous injection of PBS, pMSCV-GFP and pMSCV-IL-35-GFP respectively. After 72 h, spleen tissues and peripheral blood were harvested for following analysis. Meanwhile, splenic T cells were isolated and incubated with 10, 30, or 50 ng/mL recombinant IL-35 factor for 24 h with the addition of anti-CD3/CD28 in vitro. T-cell subsets were assessed by Fluorescence activated cell sorting (FACS) and related cytokines together with effector molecules were determined by real time PCR. RESULTS: Western blotting confirmed a 52 kDa band in the cell lysate of HEK 293T transducted with pMSCV-IL-35-GFP plasmid, indicating a successful expression of IL-35. Ebi3 and IL-12A, two subunits of IL-35, could be identified 72 h post DNA injection. IL-35 upregulation in vivo effectively inhibit CD4+ and CD8+ T cell proliferation and Th1 cytokine secretion. Effector molecules of CD8+ T cells were also remarkably suppressed. On the contrary, high level of IL-35 significantly induced CD4+ CD25+ Tregs and Th2 enhancement. The in vitro study provided similar results. CONCLUSION: The results indicated Th1 and CD8+ T cell inhibition and Th2 and Tregs bias in the presence of IL-35 under a normal state which partly contributed to its therapeutic potential.

Genomic instability in adult men involved in processing electronic waste in Northern China.

BACKGROUND: Managing and recycling electronic waste (e-waste), while useful and necessary, has resulted in significant contamination of several environments in China. The area around Tianjin, China has become one of the world's largest e-waste disposal centers, where electronics are processed by manually disassembly or burning, which can result in serious exposure of workers to a multitude of toxicants. OBJECTIVE: The present study assessed potential genomic damage in workers involved in recycling e-waste. METHODS: To detect cytogenetic and DNA damage, chromosomal aberrations (CA), cytokinesis blocking micronucleus (CBMN) and the comet assay were performed. Concentrations of some trace elements, markers of oxidative stress and polychlorinated biphenyls (PCBs) in whole blood or serum were measured, and relationships among the markers described above, age, and duration of exposure were analyzed. The profiles of expression of genes in lymphocytes in peripheral blood were assessed to determine the status of the regulation of genes involved in genome stability. RESULTS: Concentrations of 28 PCB congeners in the whole blood of the exposed group were significantly (P<0.001) greater than those in the control individuals. Frequency of CA (8.01%) and CBMN (26.3‰) in lymphocytes and the level of DNA damage in the lymphocytes and spermatozoa of the exposed men were also significantly (P<0.0001) greater than those of the controls. There were significant relationships between CA, CBMN, DNA damage and duration of exposure. Concentrations of malondialdehyde (MDA) and lead (Pb) in the blood serum were significantly greater, but activities of superoxide dismutase (SOD), glutathione (GSH) and concentrations of calcium (Ca) and magnesium (Mg) were lower in the serum of the exposed men. MDA, Pb, Ca and Mg were associated with the duration of exposure to handling e-waste. In males involved in handling of e-waste, there were 13 genes - ATM, ATR, ABL1, CHEK1, CHEK2, GADD45A, CDK7, GTSE1, OGG1, DDB1, PRKDC, XRCC1 and CCNH - for which expression of mRNA was up-regulated and 7 genes - BRCA1, GTF2H1, SEMA4A, MRE11A, MUTYH, PNKP and RAD50 - for which the expression of mRNA was down-regulated. CONCLUSIONS: A strong correlation between indicators of damage of DNA, which could result in instability of the genome, and duration of processing e-waste was observed. If proper procedures are not followed, there are significant risks to the health of the individuals involved in such activities.

Long-term Persistent Organic Pollutants Exposure Induced Telomere Dysfunction and Senescence-Associated Secretary Phenotype.

Environmentally persistent organic pollutant (POP) is the general term for refractory organic compounds that show long-range atmospheric transport, environmental persistence, and bioaccumulation. It has been reported that the accumulation of POPs could lead to cellular DNA damage and adverse effects of on metabolic health. To better understand the mechanism of the health risks associated with POPs, we conducted an evidence-based cohort investigation (n = 5,955) at the Jinghai e-waste disposal center in China from 2009 to 2016, where people endure serious POP exposure. And high levels of aging-related diseases, including hypertension, diabetes, autoimmune diseases, and reproductive disorders were identified associated with the POP exposure. In the subsequent molecular level study, an increased telomere dysfunction including telomere multiple telomere signals, telomere signal-free ends, telomere shortening and activation of alternative lengthening of telomeres were observed, which might result from the hypomethylated DNA modification induced telomeric repeat-containing RNA overexpression. Moreover, dysfunctional telomere-leaded senescence-associated secretory phenotype was confirmed, as the proinflammatory cytokines and immunosenescence hallmarks including interleukin-6, P16INK4a, and P14ARF were stimulated. Thus, we proposed that the dysfunctional telomere and elevated systemic chronic inflammation contribute to the aging-associated diseases, which were highly developed among the POP exposure individuals.

[Genetic mutation and clinical features of osteogenesis imperfecta type V].

OBJECTIVE: To explore genetic mutations and clinical features of osteogenesis imperfecta type V. METHODS: Clinical record of five patients (including one familial case) with osteogenesis imperfecta type V were retrospectively analyzed. Peripheral blood samples of the patients, one family member, as well as healthy controls were collected. Mutation of IFITM5 gene was identified by PCR amplification and Sanger sequencing. RESULTS: A heterozygous mutation (c.-14C>T) in the 5-UTR of the IFITM5 gene was identified in all of the patients and one mother. The clinical findings included frequent fractures and spine and/or extremities deformities, absence of dentinogenesis imperfecta, absence of hearing impairment, and blue sclera in 1 case. Radiographic findings revealed calcification of the interosseous membrane between the radius-ulna in all cases. Hyperplastic callus formation was found in 3 cases. Four had radial-head dislocation. CONCLUSION: A single heterozygous mutation c.-14C>T was found in the 5-UTR of the IFITM5 gene in 5 patients with osteogensis imperfecta type V. The patients showed specific radiological features including calcification of interosseous membrane, hyperplastic callus formation, and radial-head dislocation.

The correlation between the expression of genes involved in drug metabolism and the blood level of tacrolimus in liver transplant receipts.

Immunosuppressive medications, such as tacrolimus and mycophenolate mofetil, are commonly used for reducing the risk of organ rejection in receipts of allogeneic organ transplant. The optimal dosages of these drugs are required for preventing rejection and avoiding toxicity to receipts. This study aimed to identify the correlation between the expression profiling of genes involved in drug metabolism and the blood level of tacrolimus in liver transplant receipts. Sixty-four liver transplant receipts were enrolled in this retrospective study. Receipts were divided into low (2-5.9 ng/ml) and high (6-15 ng/ml) tacrolimus groups. Clinical assessment showed that the blood level of tacrolimus was inversely correlated with the liver function evaluated by blood levels of total bilirubin and creatinine. Compared to the high tacrolimus group, expression levels of six cytochrome P450 enzymes, CYP1A1, CYP2B6, CYP3A5, CYP4A11, CYP19A1, and CYP17A1 were significantly higher in the low tacrolimus group. The expression levels of these genes were negatively correlated with the tacrolimus blood level. Enzyme assays showed that CYP3A5 and CYP17A1 exerted direct metabolic effects on tacrolimus and mycophenolate mofetil, respectively. These results support clinical application of this expression profiling of genes in drug metabolism for selection of immunosuppressive medications and optimal dosages for organ transplant receipts.

The Effect of Traditional Chinese Formula Danchaiheji on the Differentiation of Regulatory Dendritic Cells.

Recently, regulatory dendritic cells (DCregs), a newly described dendritic cell subset with potent immunomodulatory function, have attracted increased attention for their utility in treating immune response-related diseases, such as graft-versus-host disease, hypersensitivity, and autoimmune diseases. Danchaiheji (DCHJ) is a traditional Chinese formula that has been used for many years in the clinic. However, whether DCHJ can program dendritic cells towards a regulatory phenotype and the underlying mechanism behind this process remain unknown. Herein, we investigate the effects of traditional Chinese DCHJ on DCregs differentiation and a mouse model of skin transplantation. The current study demonstrates that DCHJ can induce dendritic cells to differentiate into DCregs, which are represented by high CD11b and low CD86 and HLA-DR expression as well as the secretion of IL-10 and TGF-ß. In addition, DCHJ inhibited DC migration and T cell proliferation, which correlated with increased IDO expression. Furthermore, DCHJ significantly prolonged skin graft survival time in a mouse model of skin transplantation without any liver or kidney toxicity. The traditional Chinese formula DCHJ has the potential to be a potent immunosuppressive agent with high efficiency and nontoxicity.

Dose regimens for Chinese adult liver transplant recipients according to the genetic polymorphisms of CYP2C9, CYP2C19, and CYP3A5 in recipients and donors.

OBJECTIVE: Genetic polymorphisms of the P450 2C9 enzyme (CYP2C9), CYP2C19 and CYP3A5 gene are known to affect the metabolism of many drugs applied in liver transplant recipients, such as warfarin, voriconazole, and tacrolimus. The aim of this study was to recommend dose regimens for the liver recipients based on CYP2C9, CYP2C19, and CYP3A5 genotypic combinations of liver transplant recipients and their donors. METHODS: 91 adult Han Chinese liver transplant recipients who underwent orthotopic liver transplantation at Tianjin First Central Hospital, China, between 2013 and 2014 were included in this study. CYP2C9*2, CYP2C9*3, CYP2C19* 2, CYP2C19*3 and CYP3A5*3, in both liver recipients and their grafted liver were tested by polymerase chain reaction-restriction fragment length polymorphism. The dose regimens for the liver recipients were recommended based on CYP genotypic combinations of the recipients and their donors. RESULTS: In the liver transplant recipients, the frequencies of CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, and CYP3A5*3 were found to be 2.75%, 4.40%, 0%, 24.18%, and 75.27%, respectively. Allele frequencies were significantly different for CYP2C9*2, CYP2C19*2, and CYP2C19* 3 (p < 0.001) when comparing the recipients with Chinese, Eastern Asians and Caucasians populations. Most dose regimens of drugs, especially of immunosuppressive drugs, should be adjusted according to the variant metabolism activity affected by the genetic polymorphisms in both recipients and their grafted liver. CONCLUSION: The dose regimens would present considerable intraand inter-patient variability in liver transplant recipients since the genetic polymorphisms of P450 enzyme in their grafted liver might complicate the metabolism of drugs in liver transplant recipients. Giving careful consideration to the CYP genotypic combinations of transplant recipients and donors in clinical dose regimens could optimize outcomes.

[Analysis of type IV osteogenesis imperfecta caused by two mutations occurred simultaneously in COL1A1 gene in a Chinese child].

OBJECTIVE: To detect potential mutations of COL1A1 and COL1A2 genes with polymerase chain reaction-high-resolution melting analysis(PCR-HRMA) in a proband diagnosed with osteogenesis imperfecta (OI). METHODS: Peripheral blood samples were collected from the proband and members of his family as well as healthy controls. The mutations were detected by PCR-HRMA and confirmed by direct sequencing. Potential effects of the mutations were predicted using softwares including PolyPhen, SIFT and Align GVGD. RESULTS: The PCR-HRMA has indicated mutations in exon 45 of the COL1A1 gene in the proband as well as his parents, which were presented as the difference in the melting curves between the patients and the control samples. Sequencing analysis confirmed that the proband has carried two heterozygous mutations (c.3235G>A, p.Gly1079Ser and c.3247G>A, p.Ala1083Thr) in exon 45 of the COL1A1 gene. Among them, c.3235G>A was predicted to have impeded alpha helix structure domain, which was inherited from the father who also had OI. c.3247G>A was inherited from mother who had a normal phenotype. All three softwares predicted that the c.3235G>A mutation can interfere with the function of the protein, while the c.3247G>A may have a benign effect by PolyPhen analysis. CONCLUSION: The study identified two mutations (c.3235G>A and c.3247G>A) occurred simultaneously in COL1A1 gene in a case. The case is the first reported in human collagen mutation database. As identified,mutation of c.3235G>A may be the major cause of the disease in the proband.

Generation of regulatory dendritic cells after treatment with paeoniflorin.

Regulatory dendritic cells are a potential therapeutic tool for assessing a variety of immune overreaction diseases. Paeoniflorin, a bioactive glucoside extracted from the Chinese herb white paeony root, has been shown to be effective at inhibiting the maturation and immunostimulatory function of murine bone marrow-derived dendritic cells. However, whether paeoniflorin can program conventional dendritic cells toward regulatory dendritic cells and the underlying mechanism remain unknown. Here, our study demonstrates that paeoniflorin can induce the production of regulatory dendritic cells from human peripheral blood monocyte-derived immature dendritic cells in the absence or presence of lipopolysaccharide (LPS) but not from mature dendritic cells, thereby demonstrating the potential of paeoniflorin as a specific immunosuppressive drug with fewer complications and side effects. These regulatory dendritic cells treated with paeoniflorin exhibited high CD11b/c and low CD80, CD86 and CD40 expression levels as well as enhanced abilities to capture antigen and promote the proliferation of CD4(+)CD25(+) T cells and reduced abilities to migrate and promote the proliferation of CD4(+) T cells, which is associated with the upregulation of endogenous transforming growth factor (TGF)-ß-mediated indoleamine 2,3-dioxygenase (IDO) expression. Collectively, paeoniflorin could program immature dendritic cells (imDCs) and imDCs stimulated with LPS toward a regulatory DC fate by upregulating the endogenous TGF-ß-mediated IDO expression level, thereby demonstrating its potential as a specific immunosuppressive drug.

Kriging-Based Parameter Estimation Algorithm for Metabolic Networks Combined with Single-Dimensional Optimization and Dynamic Coordinate Perturbation.

The metabolic network model allows for an in-depth insight into the molecular mechanism of a particular organism. Because most parameters of the metabolic network cannot be directly measured, they must be estimated by using optimization algorithms. However, three characteristics of the metabolic network model, i.e., high nonlinearity, large amount parameters, and huge variation scopes of parameters, restrict the application of many traditional optimization algorithms. As a result, there is a growing demand to develop efficient optimization approaches to address this complex problem. In this paper, a Kriging-based algorithm aiming at parameter estimation is presented for constructing the metabolic networks. In the algorithm, a new infill sampling criterion, named expected improvement and mutual information (EI&MI), is adopted to improve the modeling accuracy by selecting multiple new sample points at each cycle, and the domain decomposition strategy based on the principal component analysis is introduced to save computing time. Meanwhile, the convergence speed is accelerated by combining a single-dimensional optimization method with the dynamic coordinate perturbation strategy when determining the new sample points. Finally, the algorithm is applied to the arachidonic acid metabolic network to estimate its parameters. The obtained results demonstrate the effectiveness of the proposed algorithm in getting precise parameter values under a limited number of iterations.

MicroRNA-214 induces dendritic cell switching from tolerance to immunity by targeting ß-Catenin signaling.

MicroRNAs (miRNAs) are known to function as negative gene regulators. Recently, miRNAs have been shown to regulate immunity processes; however, the mechanism is unclear. The role of microRNA-214 (miR-214) in dendritic cell (DC) maturation has not been investigated. We found that the miR-214 level was correlated with the maturation of DCs and inflammatory cytokine secretion, as depressed miR-214 levels induced DC tolerance. We also identified ß-catenin as a target gene of miR-214 and demonstrated its association with Treg cell differentiation. MiR-214 regulates gene expression by binding to the 3'UTR of ß-catenin. The results suggest that ß-catenin is a critical regulator of tolerance in DCs via miR-214. The expression of miR-214 could be a potential therapeutic strategy in organ transplantation or autoimmunity patients.

Identification of gene mutation in patients with osteogenesis imperfect using high resolution melting analysis.

Osteogenesis imperfecta (OI), a congenital bone disorder, is caused by mutations in COL1A1 and COL1A2 genes, leading to deficiency of type I collagen. The high resolution melting (HRM) analysis has been used for detecting mutations, polymorphisms and epigenetic alteration in double-stranded DNAs. This study was to evaluate the potential application of HRM analysis for identifying gene mutations in patients with OI. This study included four children with OI and their parents and fifty normal people as controls. Blood samples were collected for HRM analysis of PCR-amplified exons and flanking DNA sequences of COL1A1 and COL1A2 genes. Direct gene sequencing was performed to validate HRM-identified gene mutations. As compared to controls, HRM analysis of samples form children with OI showed abnormal melting curves in exons 11 and 33-34 of the COL1A1 gene and exons 19 and 48 of the COL1A2 gene, which indicates the presence of heterozygous mutations in COL1A1 and COL1A2 genes. In addition to two known mutations in the COL1A2 gene, c.982G > A and c.3197G > T, sequencing analysis identified two novel mutations in the COL1A1 gene, c.2321delC and c.768dupC mutations, which function as premature stop codons. These results support future studies of applying HRM analysis as a diagnostic approach for OI.

Integrated analysis of transcription factor, microRNA and LncRNA in an animal model of obliterative bronchiolitis.

Obliterative bronchiolitis (OB) is characterized by sub-epithelial inflammatory and fibrotic narrowing of the bronchioles, and it is the predominant factor limiting long-term survival after lung transplantation. To explore molecular mechanism of OB, we investigated the interaction of transcription factor (TF), microRNA, long noncoding RNA (lncRNA), and gene expression in the mice model of OB by integrated analysis of TF array, miRNA microarray, and lncRNA and mRNA microarray. After 28 days of orthotopic tracheal transplantation in mice, 42 TFs were significantly up-regulated in allogeneic graft compared to syngeneic graft; 62 miRNAs including miR-376-5p were up-regulated and 17 miRNAs including miR-338-3p were down-regulated over 2-fold; 137 mRNAs were down-regulated and 129 mRNAs were up-regulated over 2-fold; 234 lncRNAs were up-regulated and 212 lncRNAs were down-regulated over 2-fold in the allogeneic model compared to that in the syngeneic control group. We further analyzed potential interaction between TFs, miRNAs, lncRNAs and target genes by different algorithms. Four differentially expressed TFs (Myc/Max, FOXO1, FOXM1, and SMAD) were predicted to regulate 3 different miRNAs, 17 mRNAs, and 16 lncRNAs. These findings suggest that modulation of altered transcription factors such as Myc/Max and FOXO1, and miRNAs such as miR-376-5p and miR-338-3p may become a preventive or therapeutic targets in the chronic lung allograft dysfunction.

Protein-DNA array-based identification of transcription factor activities differentially regulated in obliterative bronchiolitis.

Lung transplantation has already become the preferred treatment option for a variety of end-stage pulmonary failure. However the long-term results of lung transplantation are still not compelling and the major death reason is commonly due to obliterative bronchiolitis (OB) which is considered as chronic rejection presenting manifests physiologically as a progressive decline in FEV1. Transcription factors (TFs) play a key role in regulating gene expression and in providing an interconnecting regulatory between related pathway elements. Although the transcription factors are required for expression of the proinflammatory cytokines and immune proteins which are involved in obliterative bronchiolitis following lung transplantation, the alterations of the transcription factors in OB have not yet been revealed. Therefore, to investigate the alteration pattern of the transcription factors in OB, we used protein/DNA arrays. Mice orthotopic tracheal transplantation model was used in this studying. In this study, we explored the activity profiles of TFs in Protein/DNA array data of tracheal tissue in 14 and 28 day after transplanted. From a total of 345 screened TFs, we identified 42 TFs that showed associated with OB progression. Our data indicate that TFs may be potentially involved in the pathogenesis of OB, and can prevent, diagnose and treat OB after lung transplantation. In development of OB, some of the TFs may have ability to modulate the transcription of inflammatory proteins such cytokines, inflammatory enzymes and so on.